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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG

Basic information

species Physcomitrella patens
transcript PP1S15_485V6.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: LOC_Os06g02380.1 (Oryza sativa), 3'ss of exon 3
gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG
                                           |   |   |  | || |    |   | ||      |   ||| || || || ||   |  ||       | ||| |  |||| | ||| |    |     || |        ||||| || || || || || || || ||||||||||| |||||||| ||||| ||| | || |||||||| ||||| |||||||||||||| ||||| || |
------------------------------------------ttttcttattgaacaagtcaactggaggtttctggattatctgtgtaacctagtt--ccagaatttgagcagaattt--tcaagtaacgat----ctctgtactg--------cagGTTGAACTGGAGGATCCTGTTGAAAATATTGGAGCTAAGTTGGTTAGGCAAGCAGCAGCAAAGACCAATGATTTAGCTGGAGATGGCACAACTACTTCTG

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 2
gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG
                                                 | ||   | |||      ||  |  ||  |    ||| |       |||||      | || |        ||   |||| | |      |||   |  |   ||  |||| ||| | || || || || ||||||||||| |||||||||||||| || ||| |||| ||||| ||||| |||||||| ||||| ||||| || || |
-------------------------------------------------tgtttgaatttgtttatgtggataggatttcatttgaat------tttgtttaagtgggttttttgggtgtttgttttgatgctttg-ttgaatttgatttggga--agGTTGAGTTGGAGGATCCGGTTGAGAATATTGGCGCCAAGTTGGTGAGACAAGCAGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACTTCGG

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: GLYMA08G18760.2 (Glycine max), 3'ss of exon 2
gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttca-attgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG
                                                   ||   | |||    | ||  |  ||  |    ||| |    |  ||    | |  | || |    | ||||   ||||| |||      |||   || |  ||   |||| ||| | || || || || ||||||||||| |||||||||||||| || ||  |||| ||||| ||||| |||||||| ||||| ||||| ||||| |
---------------------------------------------------tttgaatttgtttacgtggataggatttcatttgaat--tgtgtttaagtggattgtttgtt---tgtgtttgtattgatgttttg-ttgaatttggtt--tggtaagGTTGAGTTGGAGGATCCCGTTGAGAATATTGGTGCCAAGTTGGTGAGACAAGCGGCTGCCAAGACAAACGACTTGGCTGGTGATGGAACCACGACCTCGG

upper sequence: PP1S15_485V6.2 (Physcomitrella patens), 3'ss of exon 2
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 3
gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG
                                    |  |  |       |||||   ||| |||  |  | ||| |     || |   ||| | |||| ||| | |        |  | || |  |   |||   ||| |               |||| ||| | || || || || ||||||||||| || || || ||||| || ||| |||| ||||||||||| |||||||| ||||| || || || || |
----------------------------------atgcctaccatctgtccttgacg-ttgagattgtc-tccagtaaatatctcaac-acaaatttgtccgtgaggc-------acttattgatgttttgttatcaccta--------------tagGTTGAGTTGGAGGATCCTGTTGAGAATATTGGTGCTAAATTAGTGAGACAAGCAGCTGCCAAGACCAACGACTTGGCTGGGGATGGGACAACAACATCTG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|162182315|gb|FC357186.1|FC357186
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162250146|gb|FC427871.1|FC427871
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|67575198|gb|BJ948022.1|BJ948022
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162153515|gb|FC329609.1|FC329609
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162183969|gb|FC359339.1|FC359339
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|208364523|gb|DC930913.1|DC930913
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162155281|gb|FC331218.1|FC331218
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|67507453|gb|BJ940335.1|BJ940335
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162153382|gb|FC329892.1|FC329892
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162175371|gb|FC352297.1|FC352297
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162171512|gb|FC347814.1|FC347814
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162157139|gb|FC333709.1|FC333709
EST:     GAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: GAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|18361532|gb|BJ193598.1|BJ193598
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAAT
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAAT
EST: gi|162256596|gb|FC432906.1|FC432906
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|67574539|gb|BJ947363.1|BJ947363
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|18341885|gb|BJ173920.1|BJ173920
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAG
EST: gi|67704538|gb|BJ964771.1|BJ964771
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162150359|gb|FC326631.1|FC326631
EST:     TCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: TCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162255427|gb|FC431841.1|FC431841
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
EST: gi|162154271|gb|FC330402.1|FC330402
EST:     AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAG                         GTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG
genomic: AGTACGGGTCTCCTAAGATTGTGAATGACGGAGTCACCGTAGCCAAGGAGgttggtgata ... tgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG
     ttataaaatctgtt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgataattttccttttgtgaggttgagtttcgattggctcaatctcttgagaattgcgatcatgattcagaagtagactgagtgacatacttgttcgtaacgattataaaatctgttcaattgacgttgaaaccgaacacgggtgatgaccagGTCGAGCTCGAAGACCCAGTGGAGAATATTGGAGCCAAGTTGGTGAGGCAGGCATCTGCGAAGACCAACGATTTGGCTGGAGATGGCACCACTACCTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG